Contacts of the helix formed by residues 163 - 177 (chain A) in PDB entry 3CAN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A GLU* 5.2 1.2 + - - +
161A THR 3.5 2.4 + - - -
162A PRO* 1.3 76.3 - - - +
164A GLU* 1.3 64.7 + - - +
165A GLU* 3.6 10.2 + - - +
166A VAL* 3.0 33.2 + - - +
167A GLN* 2.9 21.1 + - - +
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PRO 3.8 0.4 + - - -
163A SER* 1.3 71.5 - - - +
165A GLU* 1.3 61.5 + - - +
167A GLN* 3.4 14.9 + - - +
168A GLN* 3.0 41.8 + - + +
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Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A SER* 3.1 8.8 + - - +
164A GLU* 1.3 80.1 - - - +
166A VAL* 1.3 58.4 + - + +
168A GLN* 3.4 5.5 + - - +
169A GLN* 2.9 59.5 + - + +
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 4.0 15.3 - - - +
110A ALA* 4.0 29.2 - - + +
162A PRO* 4.0 16.4 - - + -
163A SER* 3.0 29.4 + - - +
165A GLU* 1.3 74.4 - - + +
167A GLN* 1.3 66.0 + - - +
169A GLN* 3.1 18.0 + - + +
170A CYS* 2.9 27.5 + - - -
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Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU* 4.3 12.8 - - + -
136A PRO* 3.5 34.1 - - + +
138A HIS* 5.5 1.4 + - - -
161A THR* 4.5 4.4 - - - +
162A PRO* 2.8 37.8 + - + -
163A SER 2.9 16.9 + - - +
164A GLU* 3.6 12.1 - - - +
166A VAL* 1.3 74.1 - - - +
168A GLN* 1.3 63.2 + - + +
170A CYS* 3.2 5.2 + - - +
171A ILE* 3.0 30.8 + - - +
183A ILE* 3.7 25.3 - - + +
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Residues in contact with GLN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLU* 3.0 36.4 + - + +
165A GLU* 3.9 4.5 - - - +
167A GLN* 1.3 75.2 + - - +
169A GLN* 1.3 60.4 + - - +
171A ILE* 3.3 17.5 + - - +
172A GLN* 2.9 29.0 + - - +
183A ILE* 4.6 16.0 - - - +
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Residues in contact with GLN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLU* 2.9 50.5 + - + +
166A VAL* 3.5 22.5 + - + +
168A GLN* 1.3 75.1 - - + +
170A CYS* 1.3 57.7 + - - +
172A GLN* 3.3 6.9 + - - +
173A ILE* 3.0 39.3 + - + +
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Residues in contact with CYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU* 4.1 18.8 - - + -
110A ALA 4.0 14.1 - - - -
112A GLU* 6.5 0.2 - - - -
115A ILE* 3.8 36.2 - - + +
134A LEU* 3.6 19.1 - - + -
166A VAL* 2.9 22.3 + - - -
167A GLN 3.5 8.1 - - - +
169A GLN* 1.3 74.2 - - - +
171A ILE* 1.3 65.9 + - - +
173A ILE* 3.4 6.2 + - - +
174A LEU* 3.2 27.9 + - - +
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Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 3.4 20.2 - - + -
167A GLN 3.0 15.8 + - - +
168A GLN* 3.6 20.2 - - - +
170A CYS* 1.3 75.8 - - - +
172A GLN* 1.3 56.1 + - - +
174A LEU* 3.4 2.1 + - - +
175A THR* 2.7 45.9 + - - +
181A ALA* 3.8 17.3 - - + +
182A THR* 3.6 38.1 - - - +
183A ILE* 3.8 14.4 - - + +
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Residues in contact with GLN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLN 2.9 17.1 + - - +
169A GLN* 3.6 9.4 - - - +
170A CYS 3.3 0.2 - - - -
171A ILE* 1.3 75.8 - - - +
173A ILE* 1.3 53.9 + - + +
175A THR* 3.3 14.7 + - - +
176A ASP* 2.7 72.1 + - - +
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Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU* 4.3 27.4 - - + +
115A ILE* 3.9 32.1 - - + +
116A LYS* 3.7 33.0 - - + -
119A ALA* 4.4 0.9 - - + -
169A GLN* 3.0 27.3 + - + +
170A CYS* 3.6 7.9 - - - +
171A ILE 3.3 0.2 - - - -
172A GLN* 1.3 76.1 - - + +
174A LEU* 1.3 64.3 + - - +
176A ASP* 3.1 17.8 + - - +
177A TYR* 3.2 32.7 + - + -
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 5.0 4.3 - - + -
115A ILE* 4.2 15.3 - - + +
118A SER* 5.0 4.0 - - - -
119A ALA* 3.7 33.7 - - + +
122A LEU* 5.1 1.3 - - + -
132A ILE* 3.9 25.4 - - + -
134A LEU* 3.9 27.4 - - + -
170A CYS 3.2 17.0 + - - +
171A ILE 3.8 3.1 - - - +
173A ILE* 1.3 78.1 - - - +
175A THR* 1.3 63.6 + - - +
177A TYR* 3.2 9.0 + - - +
178A GLY 3.4 0.2 + - - -
179A LEU* 3.1 31.4 + - + +
181A ALA* 3.8 28.5 - - + -
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Residues in contact with THR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ILE* 2.7 32.5 + - - +
172A GLN* 3.6 17.9 - - - +
174A LEU* 1.3 75.1 - - - +
176A ASP* 1.3 58.1 + - - +
178A GLY* 2.9 20.6 + - - -
179A LEU 3.6 15.0 + - - +
181A ALA* 5.1 4.7 + - - +
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Residues in contact with ASP 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLN* 2.7 59.6 + - - +
173A ILE* 3.1 10.3 + - - +
175A THR* 1.3 72.3 - - - +
177A TYR* 1.3 63.8 + - + +
178A GLY 3.2 1.0 + - - -
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LYS* 4.2 19.9 - - + +
119A ALA* 3.4 26.0 - - + -
120A GLU* 2.6 50.2 + - + -
123A ALA* 3.6 23.7 - - + +
128A HIS* 5.0 2.6 - - - -
173A ILE* 3.2 33.7 + - + -
174A LEU 3.2 8.3 + - - +
175A THR 3.2 1.2 - - - -
176A ASP* 1.3 81.2 - - + +
178A GLY* 1.3 60.1 + - - +
179A LEU* 3.4 7.6 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il